schrodinger.application.desmond.torsion_related module¶
- class schrodinger.application.desmond.torsion_related.TorsionPotential(a1, a2, a3, a4, cms, lig_atoms, results=None, calc_tors=True)¶
Bases:
object
A class to contain the atom numbers for each torsion
- dih = None¶
- __init__(a1, a2, a3, a4, cms, lig_atoms, results=None, calc_tors=True)¶
- set_color(col)¶
- get_color()¶
- set_ligand_from(lfrom)¶
- set_ligand_to(lto)¶
- get_angles()¶
- set_rbpotential(rbp)¶
- get_potential()¶
- init_ff(st, atom_list)¶
This function initializes torsion force field parameters relevant to the ligand. Ligand is defined by a list of atoms.
- Parameters
st (
structure.Structure
) – structure object for all moleculesatom_list (list) – list of ligand atom indices
- class schrodinger.application.desmond.torsion_related.BondRotator(st, rb_atoms, angle_diff=10, ff=16, debug=False, canonicalize=True, sampling=True)¶
Bases:
object
perform RB scan
- __init__(st, rb_atoms, angle_diff=10, ff=16, debug=False, canonicalize=True, sampling=True)¶
- potential(conf=None, degree=True)¶
get potential energy corresponding to ‘conf’ :param conf: conformation in degrees to get corresponding potential :type conf: float
:rtype float
- search_and_scan(st: schrodinger.structure._structure.Structure)¶
Get best profile by using fast3d to generate multiple initial coordinates.
self.results
to contain the best profile.
- getRotEnergy(offset=False)¶
- schrodinger.application.desmond.torsion_related.get_old2new(st, prop='i_m_original_index')¶
Get dictionary for atom-level property ‘prop’ as a key, and return it’s new atom index (aid)
- exception schrodinger.application.desmond.torsion_related.IncompleteFragmentError¶
Bases:
Exception
- schrodinger.application.desmond.torsion_related.get_rb_potential(cms_model, lig_aids, a1, a2, a3, a4)¶
- schrodinger.application.desmond.torsion_related.rb_potential_from_struct(lig_st, tor_sys_idx)¶
Creates bond rotator object to calculate torsional potential for a given structure. The input structure should have ‘ORIGINAL_INDEX’ property.
- Parameters
lig_st (structure.Structure) – ligand structure
tor_sys_idx (list[int]) – list of atom indices to define torsion
- Returns
bond rotator object
- Return type
- schrodinger.application.desmond.torsion_related.get_rb_torsions_potential(cms_model, lig_aids, a1, a2, a3, a4)¶